Prokaryote genomes exhibit a wide range of GC contents and codon usages, both resulting from an interaction between mutational bias and natural selection. In order to investigate the basis underlying specific codon changes, we performed a comprehensive analysis of 29 different prokaryote families. The analysis of core gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly expressed genes presented the most optimized codon usage, the singletons contained the less selectively favored codons. The results showed that usually codons with the highest translational adaptation were preferentially enriched. In agreement with previous reports, a C bias in 2- to 3-fold pyrimidine-ending codons, and a U bias in 4-fold codons occurred in all families, irrespective of the global genomic GC content. Furthermore, the U biases suggested that U₃-mRNA–U₃₄-tRNA interactions were responsible for a prominent codon optimization in both the most ancestral core and the highly expressed genes. A comparative analysis of sequences that encode conserved (cr) or variable (vr) translated products, with each one being under high (HEP) and low (LEP) expression levels, demonstrated that the efficiency was more relevant (by a factor of 2) than accuracy to modeling codon usage. Finally, analysis of the third position of codons (GC3) revealed that in genomes with global GC contents higher than 35 to 40%, selection favored a GC3 increase, whereas in genomes with very low GC contents, a decrease in GC3 occurred. A comprehensive final model is presented in which all patterns of codon usage variations are condensed in four distinct behavioral groups.

中文翻译：

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生命原核树中的密码子使用优化：如何在具有不同表达水平和保守程度的序列域中差异选择同义密码子。

原核生物的基因组表现出广泛的GC含量和密码子用法，这两者都是由突变偏倚和自然选择之间的相互作用导致的。为了调查特定密码子变化的基础，我们对29个不同的原核生物家族进行了全面分析。对每个家庭谱系中祖先增加的核心基因集的分析表明，密码子使用逐渐变得更适应tRNA库。正如先前报道的那样，高表达基因提供了最优化的密码子使用方式，而单子包含的选择性较弱的密码子。结果表明，通常具有最高翻译适应性的密码子被优先富集。与先前的报道一致，C偏向2至3嘧啶末端的密码子，不论全球基因组GC含量如何，所有家族中都出现4倍密码子的U偏向。此外，U偏见表明U₃ -mRNA–U ₃₄ -tRNA相互作用是最祖先核心和高表达基因中显着的密码子优化的原因。编码保守（cr）或变量（v r的序列的比较分析）的翻译产品，每个产品都处于高（HEP）和低（LEP）表达水平，这表明效率与模拟密码子使用的准确性更相关（系数为2）。最后，对密码子第三个位置（GC3）的分析表明，在总体GC含量高于35％至40％的基因组中，选择有利于GC3的增加，而在GC含量极低的基因组中，GC3的降低。提出了一个综合的最终模型，其中所有密码子使用变化的模式都被浓缩为四个不同的行为组。